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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttggttgacttcttgagtgttttacctttatgcaatttagactaacaagttgagtgtggtattttgctaagatctttatgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA

Basic information

species Vitis vinifera
transcript Vv06s0004g03940.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA11G15480.1 (Glycine max), 3'ss of exon 12
--tgcttggttgacttcttga--gtgttttacctttatgcaatttagactaacaagttgagtgtggtattttgctaagatctttatgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
| | | | |||| | || ||| | | | | | | | || ||| |||| | || | ||| | |||| |||||| |||| ||||||| |||| ||| || || | ||||| ||||| ||| | ||||||||||| || ||||| |||||||||||||||||||||
cctaaattaaaaatatgttgacaaattcctaaattttaattctctgaaattattttcccaattcaataattt-ctaa---cgggataggggttgttgctcgcagTTACAACAGAGGTTGGTTTTATCACAAAGAACATCGTTTATGGTTAATAAGAGTTCCCAACATGGAGCCGCTGGTTAAAACAAACACATATGAGAGAGGA

upper sequence: Vv06s0004g03940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G07970.2 (Glycine max), 3'ss of exon 10
tgcttggttgacttcttgagtgttttacctttatgcaatttagactaacaagttgagtgtggtattttgctaagatcttt----atgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
| | ||| |||| || |||||| | | | | | || ||| ||| | | ||| | |||| |||||| |||| ||||||| |||| ||| || || ||||||| ||||| ||| | ||||||||||| || ||||| ||||||||||| |||||||||
----tcctaaactaaaaatatgttgacaaattcctaaatttaattctctgaaattgttttcccaattcaataatttctaacgaggtaggggttgttgctcgcagTTACAACAGAGGTTGGTTTTATCACAAAGAACATCGTTTGTGGTTTATAAGAGTTCCCAACATGGAGCCGCTGGTTAAAACAAACACATACGAGAGAGGA

upper sequence: Vv06s0004g03940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G40650.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------tgcttggttgactt---cttgagtgttttacct-ttatgcaatttagactaacaagttgagtgtggtatttt-gctaagatcttta-----tgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
| || ||| | || || |||| ||| | | |||| | | ||| | ||| ||| | || | || ||| | | ||| |||||| ||||| || || ||||||| || | |||||| || | ||||| ||||| ||| | ||||||||||| ||||| || ||||||||||| |||||||||
gtatgtattcactcacatgcagcttttttgatgtgttgtttttggatgatttggtcttagttctgagttaatttagtctagagtatttaaattgttattgtgtatgtgtgtgtgtgtttattgttttatcatagcaataattattaacaaggaagggttgttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA

upper sequence: Vv06s0004g03940.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G04780.1 (Glycine max), 3'ss of exon 13
------------------------------------------------tgcttggt-tgacttcttgagtgtttta-cctttatgcaatttagactaacaagttgagtgtg-gtattttgctaa-gatctttat-gaca-------tctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
||||| | | |||| | | ||||| || || ||||| | | | || ||||| || | || || || |||| ||| | ||| |||||| ||||| || || ||||||| || | |||||| || | ||||| ||||| ||| | ||||||||||| ||||| || ||||||||||| |||||||||
gtatgtattcactcacatgcacccttttttgttgtgttgtttttggatgatttggtcttagttctgaattattttagtctgtagagtatttaaattgttattctgtgtgtgtgtttattaatagcaataattattaacaagggtgggttattgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110375098|gb|EC940056.1|EC940056
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
EST: gi|34361715|gb|CF403300.1|CF403300
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
EST: gi|110429086|gb|EC995574.1|EC995574
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
EST: gi|110361031|gb|EC924481.1|EC924481
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
EST: gi|110414858|gb|EC980718.1|EC980718
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
EST: gi|110715851|gb|EE094372.1|EE094372
EST:     CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACT                         CTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG
genomic: CATGCCGAAAGACGAAGCCCAATTATATGCTGCAAATGAACTgtatgttttc ... ttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaagttgagtgtggtattttgctaagatctttatgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
 gactaac  putative branch site (score: 1)
 tctcttgtt  putative PPT
 atctttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttggttgacttcttgagtgttttacctttatgcaatttagactaacaagttgagtgtggtattttgctaagatctttatgacatctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
tgcttgg
- - - - - - - - tgagtgt
- - - - - - - - - - - - - - - -tatgcaa
- - - - - - - - - - - - - - - - - - - - - - ctaacaa